Fixbug: SAMPLES columns

tasks/VEP.wdl

@@ -34,17 +34,17 @@ task VEP {
 
 
     # Judge the SAMPLE info of vcf file
-    tumor_id=`awk -F'\t' '{if($1~"^#CHROM"){print $10}}' ${vcf}`
-    normal_id=`awk -F'\t' '{if($1~"^#CHROM"){print $11}}' ${vcf}`
-
-    if [ $normal_id ]; then
-      SAMPLE_vcf2maf="--tumor-id $tumor_id --normal-id $normal_id"
-      SAMPLE_vcf2vcf="--vcf-tumor-id $tumor_id --vcf-normal-id $normal_id"
+    sample_col_1=`awk -F'\t' '{if($1~"^#CHROM"){print $10}}' ${vcf}`
+    sample_col_2=`awk -F'\t' '{if($1~"^#CHROM"){print $11}}' ${vcf}`
+    
+    if [ $sample_col_2 ]; then # This situation means there are pairs
+      SAMPLE_vcf2maf="--tumor-id $sample_col_2 --normal-id $sample_col_1"
+      SAMPLE_vcf2vcf="--vcf-tumor-id $sample_col_2 --vcf-normal-id $sample_col_1"
       cp ${vcf} ${sample_id}.tmp1.vcf
-    else
-      SAMPLE_vcf2maf="--tumor-id $tumor_id"
+    else # Tumor-only or normal-only
+      SAMPLE_vcf2maf="--tumor-id $sample_col_1"
       # Add a column and remove it after vcf2vcf
-      SAMPLE_vcf2vcf="--vcf-tumor-id $tumor_id --vcf-normal-id $tumor_id"
+      SAMPLE_vcf2vcf="--vcf-tumor-id $sample_col_1 --vcf-normal-id $sample_col_1"
       awk -F'\t' 'OFS="\t" {if($1!~"^##" && length($11)==0) $11=$10; print $0}' ${vcf} > ${sample_id}.tmp1.vcf
     fi
 
@@ -56,7 +56,7 @@ task VEP {
     $SAMPLE_vcf2vcf \
     --ref-fasta ${ref_dir}/${fasta}
     
-    if [ $normal_id ]; then
+    if [ $sample_col_2 ]; then
       cp ${sample_id}.tmp2.vcf ${basename}.norm.vcf
     else
       cut -f 1,2,3,4,5,6,7,8,9,10 ${sample_id}.tmp2.vcf > ${basename}.norm.vcf